BU to track, predict soybean disease in huge three-year study

Charlotte Smith works in the lab, where she'll be helping analyze the DNA of various soybean diseases this summer.

A three-year research project starting this summer will help soybean farmers predict disease before it strikes their crops.

Brandon University’s Dr. Bryan Cassone has received $112,509 from the Manitoba Pulse & Soybean Growers (MPSG) to genetically analyze whole fields of soybean plants, looking for the distinctive DNA markers of disease, even well before symptoms appear.

“Prevention is always the first and foremost measure for disease control,” says Dr. Cassone, who joined the BU Biology department as an assistant professor last year. “However, this is only possible if we know what is infecting our fields and can develop early diagnostic tools and control strategies, which vary dramatically based on the type of pathogen. The reason why many disease outbreaks occur is a lack of this knowledge.”

He’s focusing on foliar diseases, which are those that invade the leaves of infected plants. Common examples in Manitoba include downy mildew and bacterial blight. With help from MPSG and Manitoba Agriculture, Food and Rural Development (MAFRD), Dr. Cassone will do two full surveys of at least 50 fields each in Manitoba looking for those and many other diseases.

“Their years of experience will also allow us to target fields particularly vulnerable to disease,” he explains. In each field, they’ll pluck a single leaf from every soybean plant, preserve it on ice or in a special preservative, and take it back to a BU lab to be fully sequenced. That will tease out DNA from any kind of disease that the soybean plant could be harbouring — including some that may have never before been detected in Manitoba.

“We go through multiple stages of ‘DNA work’ before we generate the data – literally hundreds of millions of pieces of DNA from the plant and the pathogens. These are pieced together for each plant like a giant DNA puzzle,” Dr. Cassone says. “The whole process will take three months or so. However, the silver lining for future disease surveillance is with these giant DNA puzzles now solved, we can easily develop sensitive diagnostic tools that can be run within the day.”

Helping him in the lab this summer is student Charlotte Smith, who’ll be entering her second year of nursing in the fall. She already has a bachelor’s degree in biological sciences under her belt.

“My ultimate career goal is to become a nurse practitioner and also to work in clinical research,” Smith says. “This project is epidemiological in nature and I think it will give me a better understanding of the way we classify disease on a large-scale population level. I hope to transfer my skills in genetic analysis to better understand the genetic patterns of disease and disease spread.”

She says this type of hands-on experience is an invaluable part of her education.

“Maybe I am biased but I feel that everyone should work or volunteer in a lab at some point in their studies whether they are pursuing a degree in science or not,” she says. “Whether it is for health, disease management or to know what foods to eat or behaviors are helpful for us, we turn to the results we see from research to make decisions. This kind of experience provides an opportunity learn to critical thinking and time management skills. You learn so much about yourself from seeing how you work with a team of people in a context where you’re working to find answers to an unknown problem.”

While some sort of lab work has always been a part of the university experience, this project involves a type and scale of high-tech work that has only recently become cost-effective to do.

“Next generation sequencing is still relatively expensive but has come down in cost dramatically over the last few years. Coupled with that, the technology has advanced exponentially,” Dr. Cassone says. “To put it into perspective, this type of project could never have been done seven or eight years ago, even in generously funded labs.”

The large-scale surveying and analytical work being tackled in this project is a continuation of Dr. Cassone’s post-doctoral research at Ohio State University, and has the potential to make a big difference to prairie soybean growers.

“Before I moved to Manitoba last September, I spent four years working on soybean. I knew growers place an emphasis on preventative research, much more so than other crops. I also knew that soybean production had exploded in the province over the last few years,” he says.

In fact, soybean farmers in Manitoba harvested a record 1.4 million tonnes of the crop last season, the fourth record-setting year in a row according to Statistics Canada, and more than 25 per cent higher than the year before. Grower interest in soybeans is expected to remain high, with 2016 having been named International Year of Pulses, which includes beans, lentils and peas.

Having a direct impact on real-world issues is something that Smith says is a bit of a thrill.

“Knowing that the work you’re doing will aid in the advancement of our society in some respect is quite motivating but it also comes with a sense of responsibility. Your work becomes an extension of your ability to create and follow your plan in a timely fashion and to be adaptable in the face of uncertainty and unexpected events,” she says. “There’s no feeling quite like that of when you’re done with an aspect of a project and you’re finally looking at the results. It’s like finding your own little piece of the puzzle!”

Among other pieces of the puzzle, Dr. Cassone says his work can help reduce the amount of spraying that producers would need to do.

“Typically the pathogen will invade the plant before symptoms develop so it can be used as an early detection tool. Certainly if the disease is caught early enough it can influence the spraying regimes used by growers,” he says. “I think it will be used increasingly as a tool for more comprehensive disease assessment rather than a mainstream surveillance method. Once a thorough ‘disease library’ has been generated, the data can be used to develop more cost-effective tools that are suitable for mainstream use.”

Smith says she can’t wait to see what she and Dr. Cassone discover over the summer.

“I think I’m most excited to hit the bench and work on the molecular aspect of the project, extracting the genetic material to see what it will reveal about crop disease conditions in the province,” she says. “It’s a great feeling to know that the results we obtain from this project will help us to better manage crop health and develop the safest and most economical methods for crop distribution in Manitoba.”

In the future, this research will help develop models to predict when and where diseases could strike — before they appear. Combining information about the number and type of pathogens with information on known environmental factors like temperature and humidity will lead to sophisticated computer models that will zero in on regions in Manitoba that are more susceptible to a given disease in a given year.

Building on the baseline of data from this project, Dr. Cassone expects to be able to determine which diseases pose the greatest risk to future Manitoba soybean yield.

“Ultimately, we want to use these models to help shape our spraying regimes and help sustain the integrity of the crop in Manitoba,” he says.